ORIGINAL: CGRetired
There is a canopy glue that applies milky but dries clear. Good stuff.. slightly pliable. I think Tower Hobbies has it.
It's called RC-56 and Tower does indeed have it:
http://www3.towerhobbies.com/cgi-bin...XR529&P=ML
I use it on all my airplane canopies. However, since it's water based I'm not sure I'd use it on a boat.